Analysis of somatic microsatellite indels identifies driver events in human tumors

Yosef E. Maruvka, Kent W. Mouw, Rosa Karlic, Prasanna Parasuraman, Atanas Kamburov, Paz Polak, Nicholas J. Haradhvala, Julian M. Hess, Esther Rheinbay, Yehuda Brody, Amnon Koren, Lior Z. Braunstein, Alan D'Andrea, Michael S. Lawrence, Adam Bass, Andre Bernards, Franziska Michor, Gad Getz

Research output: Contribution to journalArticlepeer-review

98 Scopus citations

Abstract

Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that exhibit high rates of mutation in the form of insertions or deletions (indels) of the repeated motif. Despite their prevalence, the contribution of somatic MS indels to cancer has been largely unexplored, owing to difficulties in detecting them in short-read sequencing data. Here we present two tools: MSMuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes containing MS indels at a higher frequency than expected by chance. Applying MSMuTect to whole-exome data from 6,747 human tumors representing 20 tumor types, we identified >1,000 previously undescribed MS indels in cancer genes. Additionally, we demonstrate that the number and pattern of MS indels can accurately distinguish microsatellite-stable tumors from tumors with microsatellite instability, thus potentially improving classification of clinically relevant subgroups. Finally, we identified seven MS indel driver hotspots: Four in known cancer genes (ACVR2A, RNF43, JAK1, and MSH3) and three in genes not previously implicated as cancer drivers (ESRP1, PRDM2, and DOCK3).

Original languageEnglish
Pages (from-to)951-959
Number of pages9
JournalNature Biotechnology
Volume35
Issue number10
DOIs
StatePublished - 1 Oct 2017
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2017 Nature America, Inc.

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